As far as stylus goes, I've only purchased one, the targus at best buy for $20. It's okay, but with nothing to compare it to, I'm probably going to buy at least one or two more. The broad tip takes some getting used to, but I'm overall happy with the preciseness it gives, which is actually better than you would expect.
As far as note taking apps go, I've purchased several. Currently, I own notes plus, note taker hd, noteshelf, ghost writer, and bamboo (free). In my opinion, they are all missing something, but not all of them are missing the same thing. Last week, my favorite was notes plus, but I really don't like how the notes are organized at all, and the ui is ugly as hell. Now this week, after a MAJOR update to the noteshelf app, it is my favorite. They greatly improved some features that were lacking, like the zoom in writing window. I really like that evernote is integrated with this app, I can send my handwritten notes directly to the evernote app as images, which are deciphered by evernote and my handwritten notes are then searchable (this does NOT work with PDF notes).
So I am using the targus stylus, writing my notes in noteshelf, and organizing them in evernote, which is synchronized across all of my devices, I really like being able to search my handwritten notes from my iPhone, really cool. I can't help but wonder why in the hell Evernote doesn't just integrate handwritten notes directly into their iPad app, it really would save all of us a bunch of trouble. Till then, this is working just fine, and I have stopped using pen and paper for the most part.